The Genetic Code is not a synonym for the Bible Code

Here’s a new paper that can be added to the growing stack of intelligent-design articles in peer-reviewed journals. Even though the authors do not use the phrase “intelligent design,” their reasoning centers on the detection of an intelligent signal embedded in the genetic code — a mathematical and semantic message that cannot be accounted for by a natural cause, “be it Darwinian, Lamarckian,” chemical affinities or energetics, or any other.

I’ve read the paper by ShCherbak and Makukov, and by golly, the Discovery Institute flack really has accurately summarized the paper: it does explicitly and clearly claim to have identified evidence of design in the genetic code! That’s newsworthy in itself, that the creationists can accurately summarize a scientific paper…as long as the results conform to their ideological expectations.

Unfortunately, what they’ve so honestly described is good old honest garbage.

Here’s the short summary of what they do: they jigger the identities of the amino acids coded for by each codon into a number, a nucleon sum. What is that, you might ask? It’s determined by adding up the number of protons and neutrons in the amino acid, which is simply the mass number of the compound. Further, you can distinguish the amino acid into it’s R group, and the atoms that make up the peptide chain proper, which he calls the B group, for standard block. The mass number of the B group is always 74, except for proline, so he transfers a hydrogen from the R group to the proline B group to bring it up to 74, and by the way, did you notice that 74 is two times 37, which is a prime number? Now if you take all the three-digit decimals with identical digits (111, 222, 333…999), and sum their digits (111=3, 222=6, 333=9, etc.) you get the quotient of the number divided by…37!!!1!!

Are you impressed yet? This is simply numerology, juggling highly derived quantities that have little to do with functional properties of the molecules to come up with arbitrary numerical relationships, and then claiming that they’re somehow significant. They also play games with the sums of the mass numbers of just the R groups for certain codons, adding or subtracting the B number, finagling things until they get numbers that are evenly divisible by their magic prime number of 37, etc. It’s pure nonsense through and through.

But every once in a while, something sensible emerges out of the murk. Here’s the logic of their argument:

To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features, but they should be inconsistent in principle with any natural process, be it Darwinian or Lamarckian evolution, driven by amino acid biosynthesis, genomic changes, affinities between (anti)codons and amino acids, selection for the increased diversity of proteins, energetics of codon-anticodon interactions, or various pre-translational mechanisms.

(1) is simply saying that there must be a pattern of some sort — if the code were purely random assignment of arbitrary nucleotides to each amino acid, it wouldn’t be much of a sign — it would suggest that the sequence is noise, not signal. (2) is the really hard part, the one where you’d have to do a lot of work: you’d have to show that natural processes did not contribute to the pattern. They do not do that. They can’t do that. They take a different and curious tack.

They literally argue that because organizing the code by their nucleon sums makes no sense and has no reasonable functional consequences…therefore it must be an artificial and intentional feature. I’ve heard this argument before. It’s called the Chewbacca defense. Ladies and gentlemen, think about it: that does not make sense! If nucleon numbers show a mathematical pattern of any kind in their relationship to codons, you must accept the existence of a designer.

However, if we can show a natural property that leads to the organization of the genetic code, then I’m afraid their argument evaporates. Even more so than building an argument on the Chewbacca defense, that is.

First, there is a pattern to the genetic code! No one has ever denied that; it’s obviously not the case that amino acids are randomly assigned to trios of nucleotides. Here’s the code:

Let’s look at one amino acid, glycine (Gly), down in the bottom right corner. The genetic code is degenerate: that means that most amino acids have multiple combinations of nucleotides that can specify them. Glycine’s codes are GGU, GGC, GGA, and GGG. Do you see a pattern? The code is actually GG_, where the third position has a lot of slack or wobble, and any nucleotide will do. We see similar cases where just the first two nucleotides are sufficient to specify leucine, valine, serine, proline, threonine, alanine, and arginine. Even with the other amino acids, there are some constraints; CA_ can identify histidine or glutamine, but if the third letter is a pyrimidine (U or C), you get histidine, while if it’s a purine (A or G), you get glutamine. There are patterns all over the place here! So of course ShCherbak and Makukov could find evidence of significant organization.

But there’s more. There are other rules associated with this pattern.

In the synthesis of these amino acids, biochemistry typically modifies a raw starting material. The first letter of the codon says something about the biosynthesis of the associated amino acid.

If the first letter is:
• C, then the amino acid is derived from alpha-ketoglutarate.
• A, then the amino acid is derived from oxaloacetate.
• T, then the amino acid is derived from pyruvate.
• G, then the amino acid is derived in a single step from simple precursors.

The second letter of the codon is correlated with chemical properties of the amino acid.

If the second letter is:
• A, then the amino acid is hydrophilic.
• T, then the amino acid is hydrophobic.
• G or C, the amino acid has an intermediate hydrophobicity.

Wait…so there’s a pattern to the genetic code, and that pattern is associated with the physical properties of the amino acids? Why, that makes sense. Chewbacca is routed! The most likely origin of the code lies in likely catalytic properties of dinucleotides; pairs of nucleotides in ancient organisms were initially functioning as proto-enzymes before they were incorporated into strings of coding information. At least that provides a historical physico-chemical route to the particular code we now have that does not require weird numerological masturbation.

It’s rather pathetic that the Discovery Institute thinks this is a beautiful piece of science. It’s not. It’s nonsense. But look how the DI spins this story:

How will evolutionists respond to this paper? It’s hard to see how they could dismiss it. Maybe they will try to mock it as old Arabian numerology, or religiously inspired (since Kazakhstan, which funded the study, is 70% Muslim). Those would be unfair criticisms. The authors have Russian names, certified doctorates, and wrote in collaboration with leading lights in the West. Or perhaps critics could argue that the authors hail from a foreign country whose name has too many adjacent consonants in it to take them seriously.

No, it appears the only way out for Darwinists would be the “Dawkins Dodge.” You may remember that one from the documentary Expelled, where Dawkins admits the possibility of panspermia for Earth, so long as the designers themselves evolved by a Darwinian process.

What’s most notable about this paper is the similarity in design reasoning between the authors and the more familiar advocates of intelligent design theory. No appeals to religion or religious texts; no identifying the designer; just logical reasoning from effect to sufficient cause. The authors even applied the “design filter” by considering chance and natural law, including natural selection, before inferring design.

If Darwinists want to go on equating intelligent design with creationism, they will now have to take on the very secular journal Icarus.

I didn’t even consider the religious or ethnic basis of this study; it didn’t come to mind at all. It is clearly simple stupid numerology, though. Look at the rationale given for all of the conclusions, which consist entirely of mathematical manipulations of arbitrary derived properties of the molecules, to arrive at a claim of prime number significance.

We certainly don’t need to invoke panspermia. Nothing in the genetic code requires design. and the authors haven’t demonstrated otherwise.

I am most amused by the cute parallelism of claiming surprise that the authors of this paper use “design reasoning” similar to that used by American Intelligent Design creationists. They’ve been slinging this slop for decades; why be impressed that another set of Intelligent Design creationists in Kazakhstan are using the same tired tropes?

I’m also not impressed with the failure of implementation of their logic. OK, they have a ‘design filter’ that they apply, but so what? Their methods failed to recognize a well-known functional association in the genetic code; they did not rule out the operation of natural law before rushing to falsely infer design.

And that last bit…I don’t care what journal it was published in. The prestige of a journal does not confer infallibility, and even the best of journals will occasionally publish crap. They will be especially likely to publish garbage when they stretch beyond the expertise of their reviewers. Icarus is a journal of planetary science that publishes primarily on astronomy and geology. This particular paper conveniently falls between the cracks — it’s a weird paper full of trivial arithmetical manipulations for arcane purposes with no scientific justification for any of its procedures. I don’t know how it got accepted for publication, other than by boring the reviewers with its incomprehensible digit fiddling.

The facts presented on this site, when combined with those now revealed to us by shCherbak, constitute invincible evidence of the truth of the Judeo-Christian Scriptures, and of the Being and Sovereignty of their Divine Author.

Yeah, numerology. Nothing but wanking over tables.

Larry Moran has more — it turns out that Uncommon Descent and Cornelius Hunter also liked this paper. Flies are drawn to shit, I guess.

The facts presented on this site, when combined with those now revealed to us by shCherbak, constitute invincible evidence of the truth of the Judeo-Christian Scriptures, and of the Being and Sovereignty of their Divine Author.

Oh my. It’s interesting how they want to make the same claims for evidence as they do for their god. Invincible, huh?

Crip Dyke, MQ, Right Reverend Feminist FuckToy of Death & Her Handmaidensays

Clever PZ has tricked you. There is much more here than just a debunking. He’s included an entire primer on real patterns in the genetic code and how they relate to the evolution and possible origin of the code.

Actually numerology is a stupendously specific test for intelligence in one of its purest forms. If you see someone talking about numerology you know that there is intelligence in the speaker, a very specific kind of intelligence where the INT/WIS ratio is undefined.

The orderliness of the genetic code is interesting. I knew about the placement of some classes of amino acids but not about the ones dealing with oxaloacetate or a-ketoglutarate. That is cool, and I did not know about it. I am definitely going to learn more about that for my Evo class.
The Nick Lane book is a very interesting trade book I recommend for everyone. Besides those features of the code, which implies some simpler earlier versions of the code from the heart of a simpler metabolism, another thing mentioned in the book that really impressed me was evidence that alkaline hydrothermal vents are capable of a-biotically forming acetyl and pyruvate, catalyzed by Ni, Fe, and S atoms that are abundant in the porous walls of the vents. So life might have started there, using those naturally occurring compounds that are still at the heart of lifes’ metabolism today. Doubly cool is that deep sea bacteria have enzymes that make acetyl and pyruvate (as we do, of course)– but in those bacteria the enzymes that make acetyl and pyruvate depend on Ni, Fe, and S atoms. Sort of makes you wonder…

Just venting there. But real science is soooo much better than creationist crap. We move forward. They do not.

The Lane book is awesome. That pattern of the genetic code implies our current 4-nucleotide, 3-codon, 20 amino acid code evolved from a simpler 2-codon code with fewer amino acids. It also provides a plausible mechanism for abiogenesis and the evolution of DNA through RNA. Well worth reading.

This paper, good dog. “Manipulate stuff to get to a number that is twice a prime number so we can do more number stuff to show an intelligence!” I’d like to have a chat with the peer reviewers.

If Darwinists want to go on equating intelligent design with creationism, they will now have to take on the very secular journal Icarus.

And

The facts presented on this site, when combined with those now revealed to us by shCherbak, constitute invincible evidence of the truth of the Judeo-Christian Scriptures, and of the Being and Sovereignty of their Divine Author.

They just contradicted themselves in the same message.

The Dishonesty Institute also just lied a lot as usual. How do they know the Designer is the xian Sky Fairy? It could be Allah, Brahma, Marduk, Zeus, Odin, the Flying Spaghetti Monster or any of dozens of other gods.

This reminds me of the old line about Lowell’s canals on Mars. That observation clearly indicated that intelligence was involved. It just didn’t tell which end of the telescope the intelligence was on.

Here, the paper doesn’t actually indicate which end of the microscope the intelligence is.

Hi, PZ. Long-time no post, but still lurk about whenever there some sciency goodness to be had. Really enjoyed your post, was reminded of a few things that are always useful in talking to folks with these sorts of “arguments”.

First, those overly-impressed by the “unreasonable effectiveness of mathematics” are apt to ignore the glaring fact that much of math is demonstrably unreal. That is, we get these abstractions that are terribly useful for describing and modeling phenomena, but they don’t necessarily exist in nature. So, right from the get-go you have to be a little suspicious about attempts to find patterns based just on mathematics.

Second, to reason from an inherent set of mathematical relationships to a claim about the physical world should require more than internal coherence on the part of the equations. After all, Einstein had some marvelous toys that instantly commended themselves to the physicists and astronomers of his day, but people like Eddington still went out and chased down an eclipse or two in order to subject Einstein’s ideas to experimental test. So, even if I thought the logic in the Icarus article to be sound, I would want to know how we proposed to test the apparent coincidence.

Third, did the Icarus editors actually run this paper by a mathematician? I’m pretty sure that the fact you can sum “three-digit series” like “111” and “222” to get an outcome is simply follows from the properties of the number set they have reified. It’s a real pattern, but it doesn’t necessarily reflect “design” any more than the fact that the digits of multiples of nine (18, 27, 36, etc.) add up to nine.

Finally, even great minds have been deceived by this sort of reasoning when they encountered unexpected coincidences in certain kinds of numbers. Eddington and Dirac both played endlessly with very large numbers,and in their case the magic prime wasn’t ’37’, but ‘137’. One could write a book about the various ingenious ways people have been able to derive 137 from various physical constants, but to my knowledge no one has ever proposed an experimental program to falsify any proposed relationships between the physical constants that relied upon the large-number coincidences.

Just suppose that this paper really is onto something, & there is irrefutable evidence for the intersession of an intelligent designer, (ID).

It then follows that ID only wanted us to have evidence for its existence when our technology has reached a certain level. However, if ID is that old Bible Bogey, Jehovah or Yahweh, then it was also trying to give some of our ancestors evidence, many centuries ago, then gave up. Not exactly the behaviour of an omnipotent, omniscient being, eh?

And another thing, now that it’s declared itself, what does it want us to do? There has not been an announcement from its Empyrean lair as to what it wants from us, so the only safe bet for the faithful is to spend all day long, every day, praying to it. I sure do hope they take that on board.

As a frequent contributor to Icarus, I am deeply disappointed by failure of the editors and/or the reviewers to reject this nonsense immediately. I lodged a complaint with Phil Nicholson, the editor-in-chief, yesterday, asking why something so outrageous had been approved. I will now be sending a copy of this over to some of the other editors as well.

@peterhuestis @5:

Icarus is a planetary science journal, covering planetary astronomy, planetary atmospheres, and planetary geology. The paper is flagrantly abusing probability and biology. In my opinion, it should have been rejected immediately as unsuitable for publication in Icarus as well as for being total nonsense.

But see! They must be right! Big Science is trying to bury it! It’s a conspiracy! The filthy atheists are up in arms about it! They just want to quash intellectual freedom! Because they hate Gawd! !!1!eleven!1!!!

I expect there will be a post from ICR to that effect in response to their champion paper being universally dissed in peer review. “How will evolutionists respond to this paper?”

So through some round about math-like exercise they come up with a prime number, and therefore…intelligent design? What exactly is the significance of a prime number? And this particular prime number as well?

Besides, they’re wrong. The only important number is 42. I read it in the book.

Even though the authors do not use the phrase “intelligent design,” their reasoning centers on the detection of an intelligent signal embedded in the genetic code — a mathematical and semantic message that cannot be accounted for by a natural cause

This summer, Tom Hanks reprises his role as Professor Robert Langdon in Dan Brown’s latest masterpiece… The Darwin Code.

PZ, now that you’ve been instrumental in taking down the TED talks by Hancock and Sheldrake, what’s your opinion on the profit generated by them ? Should TED keep profit generated from pseudoscientific talks you opposed, or rather donate that to some worthy cause ? Speak your mind as loud and clear as you did on Sheldrake and Hancock’s talks, don’t be afaraid ! I’d love to hear about it !

But please, direct you’re response to TED, not me – I have no way of influencing them. So if you feel confident telling them what to talk about, you’ll surely feel confident telling them where to direct their money. Go ahead, they shouldn’t make money off of pseudoscientific babble anyway. So please, keep on being a hero and get in their face, tell them where to put the money they generated by presenting pseudoscientific talk to the public. Go you cute, hairy little beaver <3

Heeeellloooo, fuck binary, there still is a corporation profiting from hosting pseudoscientific talks, now moreso than ever, after being forced to limit these talks to a small, hardly detectable corner of the web. I personally think that takes priority over random BS – they’re still out there, making profit from hosting Hancock and Sheldrake. Because they didn’t take the talks down, they created a big fuzzy discussion about them. Best way to take the talks down would be to call them out all over the web – no profit from woo, period. TAKE IT DOWN.

Numerical discussions for example. Admittedly not so random after this particular blog post, but I also wanted to draw some attention to the whole TED affair. Shame on me. But really, the only point the woomeisters got over there after hundreds of comments is the accusation that TED still makes money from something they don’t agree with. I personally find that ridiculous, and you guys can belittle me a or go over there and call TED out on the hypocrisy of taking down talks but still cashing in on them. I don’t give a fucking shit after this any more, I am done with this to be honest. So go ahead, call out TED for profiting of woo or don’t give a fuck.I’m donejust quietly mumble in your corner of the web.

Clever PZ has tricked you. There is much more here than just a debunking. He’s included an entire primer on real patterns in the genetic code and how they relate to the evolution and possible origin of the code.

Damn. That actually would be great. I will have to read later, when sober. My knowledge on genetics is, admittedly, lacking.

Sorry but there’s no mention of the money problem I addressed. Remember what my initial post was about…TED still made money off of Hancock and Sheldrake. Pushing away their talks but keeping the money is despicable. TED should clearly be disassociating themselves from any content along with any profit, or the cannot be taken seriously. That Mr. Myers or Coyne would allow that really baffles me.

As long as TED says they distance themseleves from the talks, fine…but doing so AND keeping the money generated by these…wow. You really wanna justify that ? You really wanna put your signature under woomeisters stating anything as long as it generates money ?

As long as TED says they distance themseleves from the talks, fine…but doing so AND keeping the money generated by these…wow. You really wanna justify that ? You really wanna put your signature under woomeisters stating anything as long as it generates money ?

No, I hate woo. But I’m just curious why you chose this post to bring it up instead of the post two down that actually discussed TED?

To you it seemed more important. When some one pointed out that there was an appropriate place for that discussion you decided to ignore that and continue trying to derail this thread. Why do you think you get to barge in to a discussion and change the subject to your liking?

Are you that rude in meat space? If you are, TY for using your real name so I know not to invite you to social gatherings.

Like I said, might be misplaced, but I had some sense of urgency about this. In other words, didn’t wanna speculate about someone maybe, eventually finding my post in some older thread. I am admittedly not that familiar with PZ’s board. Shame on me if it makes you happy.

“What makes you think they have the power to allow or not allow it?”

Are you playing dumb ? Do you think I was ‘literally’ referring to allowing, or more generally to the ubiquitous figure of speech which any twelve-year-old is familiar with – meaning, are they gonna let this pass by without protest ? Well, so far, they haven’t protested to TED for profiting from woo, which makes me sad.

“No, I hate woo. But I’m just curious why you chose this post to bring it up instead of the post two down that actually discussed TED?”

Again, unfamiliarity with your message boards. Does that disqualify my concerns ? Did I cause anyone on here any harm ?

Most importantly to me, again…should TED be allowed to placate the public but still profit from the talks in question ?

Feel free to take my posts to a section of this site where they are deemed as “appropriate”, where they can freely be bashed. Sorry if I picked the wrong post to start this debate. May the old ones direct me to a place more appropriate.

Until that, I still haven’t heard how you justify keeping the money generated by these talks, as opposed to giving it to more scientific causes (apart from being just, a really cool robin hood thing to do, wouldn’t it be ?). But alas, if you don’t feel these are points worthy of addressing, keep stabbing on minor aspects of my postings. I’m off to bed.

You never, ever, barged into a discussion, meatspace or not ? You never ever felt the topic was important enough to just burst and interrupt ? Wow, are you alive ?

Mind you, I might have bursted in, but I never insulted anyone. NEVER CALLED ANYONE NAMES; NEVER INSULTED ANYONE ! To me the most important aspects of discourse. Might have gotten carried away, but arguably by most sources on debate kept my cool. Now, would you award me with some polieness and state something relevant to my initial inquiry, which is important to me as ever ?

Eva, I didn’t insult you or call you any names. I made an accurate observation of your behavior as being rude. I also pointed out that you were lying when you said you were sorry for interrupting, which you confirmed by ignoring the Rev. BigDumbChimp’s gentle admonishment to move your conversation to a thread where it would be on topic.

Nevermind, people before erikthebassist did. Point is – I didn’t start the rude thing. Now go over to the thread deem appropriate by the Pharyngula cops and add something valuable to the discussion, or don’t.

Bump for robro #18.
Why pick on 37? I’ve never quite grasped the fascination with prime numbers. Sure they are quaint in their indivisible-ness, but why should 37 be the stamp of the almighty dog? Surely it should be a number me tinned in one of the holy rags. Or 666, or whatever the devils number was before it was apparently mistranslated. Or 69. If 69 turned up in my numerological tea I’d take far more interest!

2. As for ruling in/out random chance, couldn’t all the possible numbers and frequencies that can be derived from this molecule disassembling be tallied and treated as a null distribution against which the occurrence of 37 is compared. Dollars to donuts other numbers, eg 1, will be faaaaar more frequent ( and thus, by their twisted logic, significant)…

“numerological masturbation” fits the bill– and it’s a widespread phenomenon amongst the clueless but calculationally competent. But there’s a more compact way to put it (coined by Tamino, of Open Mind), which is worth adopting as standard terminology for both its wit and pithiness: mathturbation.

PZ, I loved this post. It was written in a way that I, uneducated for the most part, can understand. I don’t have anything to add, but did want to express my gratitude. I can use your expertise to counter some nonsense coming from Intelligent Design propagandists in my small sphere of influence.

Here’s the short summary of what they do: they jigger the identities of the amino acids coded for by each codon into a number, a nucleon sum. What is that, you might ask? It’s determined by adding up the number of protons and neutrons in the amino acid, which is simply the mass number of the compound. Further, you can distinguish the amino acid into it’s R group, and the atoms that make up the peptide chain proper, which he calls the B group, for standard block. The mass number of the B group is always 74, except for proline, so he transfers a hydrogen from the R group to the proline B group to bring it up to 74, and by the way, did you notice that 74 is two times 37, which is a prime number? Now if you take all the three-digit decimals with identical digits (111, 222, 333…999), and sum their digits (111=3, 222=6, 333=9, etc.) you get the quotient of the number divided by…37!!!1!!

*Sigh* I thought we had settled this – it is well known that the answer to the mystery of life and the meaning of everything is 42. How dare these 37-ist heretics deny the wisdom of the Hitchhiker’s Guide to the Galaxy?

Yes, I know this joke has already been used several times upthread in various forms.

It is rapidly approaching the point where finding original means to mock the foolishness of creationists is far more difficult and interesting than flying rhetorical 747s through the gaping holes in their arguments.

Isn’t it funny how these people never look at the supposed design, with all the errors and waste and redundancy and plain old mind-boggling stupidity and go “Y’know, if there’s a designer he’s kind of a fuck up?”

I seem to recall one of the discoverers of DNA’s helix structure saying that he could design a simpler, less error-prone code with no degeneracy, for example. If a puny human could think it up, why not a supposed hyper-intelligent designer?

Hi. Speaking of pseudo-science: creationists say that Phylogeny doesn’t test for the mechanisms (mutations + natural selection) by wich some features come about. But then I saw a response to that (by Nick Matzke) that stated: «Descent with modification is the mechanism, and it is basically proven when phylogenetic analysis indicates strong statistical tree signal in the data. Within the broad mechanism of descent with modification, we have mechanisms of modification, namely mutations and the population genetic mechanisms which spread mutations in the population, such as drift and selection. These are all extremely well-studied mechanisms whose existence is not at all in doubt. And the sequence substitution models used in phylogenetics nowadays actually explicitly take the different relative probability of different sorts of mutations into account. And these sequence substitution models are also tested as standard parts of phylogenetic analysis». I think he’s arguing that phylogeny tests the mechanisms of evolution – can someone explain why/why not phylogenetics can test it?

Pechmann & Frydman showed with tedious analysis that the frequency of codon usage (e.g. how often one of the 6 Arg codons is used and different species sometimes prefer different codons over the other 5) can be strictly conserved at certain locations among species. So, although all put an arginine in the same position of the peptide chain and all could use any codon they like, they always use the codon with the lowest frequency, which the authors equate with lowest incorporation rate. (here comes the speculation part) This points to an importance of lower translation rates at certain spots during protein folding in order to establish the meaningful structure of the peptide chain when coming off the ribosome. This is like a nanosecond break for the ribosome which allows the previously synthesized peptide to form a secondary structure or something else to happen.

I would have liked to see an additional analysis of pivotal proteins (e.g. cytC or the RecA homologs) across all kingdoms because this study was done in yeast strains only but this might be another paper.

I have wondered for a long time why ID has any fans at all, given that the best it could do is imply a designer. It can’t verify a designer: random is random and it doesn’t follow that a pattern could not occur randomly. It could never verify who the designer is (unless they find Slarty’s signature on the glacier or the designer’s telephone number or something else more concrete than what they appear to look for.)

It doesn’t even follow that a designer would be a deity. At this point in our history, we do not understand enough to rule out the possibility that a universe can be created artificially. The designer could be a grad student in a parent universe. (If that’s true, we probably do need to fear the coming of the great chloroform container.)

I realize I am asking for irrational people to be logically consistant, but I don’t think it is unreasonable to ask this of people outside ID such as the publisher.

Sorry about the rant (particularly if there is an appropriate place for this and this thread isn’t it.)

PZ, we need more articles like this :) You may not be all that great at religion or philosophy, but when it comes to science, you’re absolutely amazing. Entries like this ignite that pure, healing fire of knowledge-seeking I’ve had smashed out of me for so long; so, thank you so much for that :)

No one ever pointed out the possibility of an earlier, two-nucleotide system to me before. And it’s absolutely fascinating that the first and second letters of the codons specify the properties that they do.

Saddest of all is how little credit these people give their “designer.” Isn’t it almost a species of blasphemy, on their part?

Even assuming that this brilliant paper is true what is to say that it is supernatural. Just because we don’t understand design does not mean that it is god playing on his numbers game board. When William Paley rightly found design in nature he postulated the it was the celestrial watchmaker. He was of course dead wrong. It was simply evolution performing natural processes found in nature. What we have here is an argument from ignorance or more specifally the old god of the gaps claim again being rolled out.

Chances are this paper will be retracted. If it is retracted the IDiots will ignore that fact. Their strategy is to get anything into a peer-reviewed journal to build up a claim that they are doing “real science” so they can use that as justification for “teaching the controversy” in K – 12 schools.

Argh. Being ill means missing so much fun. An actual unironic use of the Chewbacca Defense… information on the genetic code that I didn’t know…

Maxim Makukov showed up on the Sb version of this thread!!! I’ve now tried to direct him here, but, as I’ve mentioned previously, the Sb spam filter doesn’t let me link here. That’s right, linking to Pharyngula from Pharyngula is forbidden, it makes submitted comments disappear without so much as an error message.

Is this really in a peer-reviewed journal?

Yes…

Like, a peer-reviewed biology journal?

…no. Here’s the paragraph from the post that you seem to have missed: “And that last bit…I don’t care what journal it was published in. The prestige of a journal does not confer infallibility, and even the best of journals will occasionally publish crap. They will be especially likely to publish garbage when they stretch beyond the expertise of their reviewers. Icarus is a journal of planetary science that publishes primarily on astronomy and geology. This particular paper conveniently falls between the cracks — it’s a weird paper full of trivial arithmetical manipulations for arcane purposes with no scientific justification for any of its procedures. I don’t know how it got accepted for publication, other than by boring the reviewers with its incomprehensible digit fiddling.”

Actually numerology is a stupendously specific test for intelligence in one of its purest forms. If you see someone talking about numerology you know that there is intelligence in the speaker, a very specific kind of intelligence where the INT/WIS ratio is undefined.

FTW!

This reminds me of the old line about Lowell’s canals on Mars. That observation clearly indicated that intelligence was involved. It just didn’t tell which end of the telescope the intelligence was on.

Here, the paper doesn’t actually indicate which end of the microscope the intelligence is.

Thread won.

Anyway, any answers comicng up ? People shouldn’t be allowed to profit from pseudoscience, so as long as TED does, let’s fuck ‘em up. If not, why ?

What makes you think you can just hijack an existing discussion here? There are two open threads on this blog, the [Lounge] and the [Thunderdome] – links can be found somewhere in the sidebar. Choose wisely.

Oh, and, all of comment 23 except the first sentence reads like you’re making fun of him. Just saying.

…Before I sent this, I actually checked if you were already in the dungeon. Nope, PZ hasn’t banned you so far, it turns out.

Everybody knows 42 is 6 * 9

…Please do explain what 54 has to do with this.

In other words, didn’t wanna speculate about someone maybe, eventually finding my post in some older thread.

There’s a list of the 15 most recent comments in the sidebar.

I am admittedly not that familiar with PZ’s board.

It’s not a board, it’s a blog!

Feel free to take my posts to a section of this site where

*facepalm*

Rev, she thinks she’s on a forum – you know, a message/bulletin board –, and she thinks you’re an administrator who can just take comments (“posts”) and move them to another thread.

*headdesk*

but I never insulted anyone. NEVER CALLED ANYONE NAMES; NEVER INSULTED ANYONE ! To me the most important aspects of discourse. […] Now, would you award me with some polieness

*headshake*

You’re too superficial for this place.

I think he’s arguing that phylogeny tests the mechanisms of evolution – can someone explain why/why not phylogenetics can test it?

Mutation frequencies and their biochemical reasons can be, and are, taken into account when making models of evolution for maximum likelihood phylogenetics, and tested against the data.

But then, I’m a phylogeneticist, and I’d say phylogenetics never really completely falsifies anything. It gives you probabilities based (sometimes quite directly, sometimes less so) on Ockham’s Razor.

When I saw the headline I was expecting that they may have discovered evidence of intelligent design in the genome of M. mycoides.

What mycoides? Extremely few genera are so widely known that you don’t need to mention their names in full even once.

PZ, we need more articles like this :) […] when it comes to science, you’re absolutely amazing.

*nodnodnod* :-)

Chances are this paper will be retracted. If it is retracted the IDiots will ignore that fact.

*chortle* Hah! The fuck they will! They’ll immediately cry about persecution, because they want to be persecuted in order that Scripture be fulfilled!

You know what would impress me if we discovered it in the genetic code? ECC-style error correction, like the ECC RAM on high-end computers. ECC works around an unfortunate characteristic of our universe, which is that very occasionally a cosmic ray will zip through your computer’s memory (or through you) and flip a bit around (or the biological equivalent).

Cosmic rays are very difficult to shield against, so in biology my understanding is that there are a bunch of error-correcting mechanisms in the transcription process to try to detect it or correct it, but they’re all fairly simple mechanisms that could have evolved (without a creator). It’s a good thing for us that our genetic error correction isn’t that good because those mutations were what enabled evolution to work in the first place.

In computers, to guard against memory errors, the first innovation was something called parity memory, where you add an extra bit per group of bits (9 bits instead of 8 being typical) and then you set the 9th bit so that the total number of 1 bits is either odd or even. Then when you read it back, if you see the wrong parity, you know one of the bits got flipped. But you can’t do anything to correct it, so typically a computer with parity memory will just crash (but at least you know something got corrupted). What’s worse, if an even number of bits gets flipped, you can’t detect it at all with parity memory.

In modern (1970’s and later) computers, if you want to guard against rare memory “mutations”, you use something called ECC memory, which typically has the same overhead as parity memory (72 bits wide instead of 64 bits, for the same 9/8 ratio as parity memory) but the 8 extra ECC bits enable you to detect and correct any single bit error in that 64 bit block, and if two bits get flipped, you can detect that and halt the system (single bit error correction / double-bit error detection, or SECDED). The bits are computed based on a type of encoding system that was named after the Bell Labs mathematician who invented it in 1950 called a Hamming code.

Now if someone were to discover anything as mathematically complicated as a Hamming code error correction system in our genetic code, that might lead me to consider intelligent design. What we do see is quite fascinating, but it shows all the hallmarks of having evolved and not having been designed in the sense that humans design things.

And for those of you building your own PC’s, if you can get a motherboard that supports ECC RAM, it’s well worth the extra expense for the protection and peace of mind that it gives you. Intel is being annoying lately by not supporting ECC RAM on their consumer Core i5 and i7 as a way to differentiate their more expensive server chips, but they do sell a few models of the Core i3 with ECC support, as do most of AMD’s CPUs.

Even if we did find something like an ECC system in the genetic code, that would still leave all the weird design blunders like the recurrent laryngeal nerve, bats having solid bones and tidal (vs birds’ flow-through) respiration systems…and the degeneracy of the code itself…to contend with.

I have to laugh at the ID proponents, because they are deliberately overlooking how horrendously badly-engineered we are, and indeed life itself is. If they really want to make that argument, I hope they’re ready to defend the dystheist, or at least dysteleological, position

The complexity of the genetic code is much greater than the complexity of a computer. If it turned out that the genetic code had something much better than ECC, I wouldn’t be surprised and it still wouldn’t be an argument for “intelligent” design.

If I’m not mistaken, gene methylation (in bacteria at least) allows for ‘historical recognition’ of a sequence–repair & editing mechanisms running into mismatches (eg. from random errors, viral intrusions, etc) along a stretch of code will use a methylated sequence as a template for overwriting the complementary sequence.

Ooh, neat :) Not being a biologist I only have a layman’s understanding of things like that. It sounds like a lot of new research avenues are opening up vis-a-vis gene expression, epigenetics, silencing, etc.

My first reaction to reading your post was “weird that bacteria would have something so sophisticated.” But that’s multicellular-crentrism (lol, check your eucaryotic privilege!). Given how long life was unicellular and what it’s been through, it makes sense bacteria would have plenty of sophisticated machinery.

As a frequent contributor to Icarus, I am deeply disappointed by failure of the editors and/or the reviewers to reject this nonsense immediately
Immediately! Even without going into details? Wow, how passionate.
I am one of the authors of the paper. And I can tell you that editors and the three reviewers (among which were one of the leading experts in the genetic code) did not fail to go deeper into details and see somewhat more than stupid numerology. By the way, confusing numerology with elementary number theory is as shameful as confusing astronomy with astrology. The problem is not with the paper ;)

It is a strange situation. Francis Crick and Leslie Orgel proposed the hypothesis of Directed Panspermia back in seventies – a scientific hypothesis by all accounts. George Marx, a Hungarian astrophysicist and SETI-proponent, noted that in such case one might expect a message in the genetic code, since, besides performing its direct biological function, the code might simultaneously serve as a very reliable and durable carrier for such a message (its durability is provided exactly by its direct biological function as it experiences exceptionally strong purifying selection). There is also absolutely nothing anti- or pseudoscientific in such assumption. But, strangely enough, when it comes to an actual attempt to retrieve the message, some researchers (particularly biologists) start to blame the whole approach as another stupid numerology. Especially if a robust candidate for such a message is found. Robust to the extent that it forms and algebraically defined set, which means that the mapping of the code itself is deduced from the pattern ensemble. In other words, the signal could not possibly be more stronger than that – it already employs informational capacity of the code entirely. But who cares? Reject that nonsense immediately!

I assume you to be Maxim Makukov, one of the authors of the paper, and the one who emailed me three hours ago. Let me to make some things clear:

1. I am not PZ. I saw your paper on the Icarus preprint server and recognized that your conclusions are not valid in terms of probability, and so lodged my initial complaint with the editors of Icarus. But I was unable to identify all problems with the biology / biochemistry. Fortunately, PZ did his own dissection and provided it above. You should be addressing him.

2. Your post does nothing to show that PZ is wrong about all of the biochemistry he has described. You merely make two fallacious arguments, “argument from authority” and “they laughed at Galileo”.

I suggest you consider PZ’s piece as another reviewer reading your paper, and as very well-supported albeit hostile review. And then you should reconsider the entire project on that basis.

Anyway, in my opinion, lodging complaint is somewhat unethical in this case. Doing that, you imply that editors were foolish enough to make such a mistake. What I would do in such case is write a paper that shows all flaws of the original paper.

**Your post does nothing to show that PZ is wrong about all of the biochemistry he has described***
Well, PZ post does nothing to show that our paper is wrong, because his post is not peer-reviewed, but our paper was reviewed by several specialist, including leading specialists in computational biology and genetic code.

Anyway, in my opinion, lodging complaint is somewhat unethical in this case. Doing that, you imply that editors were foolish enough to make such a mistake.

I do not imply that the editors of Icarus are foolish – many of them are my teachers and professional colleagues, and I know that they are very smart and capable. I assert that there was a failure of peer review / editorial oversight in this particular case, based on your paper being nonsense and being accepted for publication. I submitted my complaint to the editors on that basis.

PZ post does nothing to show that our paper is wrong

Incorrect. He shows how the patterns in the RNA codon table traces to the chemical properties of the different amino acids, referencing various parts of the biochemical literature and providing a link to Lane’s popular-level description as a starting point.

All prior evidence says that P(artificial) is much much less than P(natural). You would have to have P(table|artificial) be much much greater than P(table|natural) in order to overcome that prior probability. And you do not have that evidence, since PZ has shown that P(table|natural) is quite high.

e.g. if P(table|artificial) = 0.01, so that there are 100 possible tables you would call artificial, and P(table|natural) = 0.004, since given the chemical rules PZ outlines above there are only a few hundred possible tables, and P(artificial) = 0.1, which is an overestimate based on previous claims of artificial signatures in biology,

P(table is artificial) = 0.01*0.1/(0.01*0.1 + 0.004*0.9) = 0.22.

Setting the prior probability to a much lower and more realistic value gives a correspondingly lower probability. If there are more possible tables you would consider artificial, then the probability also goes down. Even setting the number of possible artificial tables at 10 and the prior probability at an outrageously large 0.5 would barely give you P(table is artificial) = 0.95.

His post is not peer-reviewed, but our paper was reviewed by several specialist, including leading specialists in computational biology and genetic code.

That is an argument from authority again, and is irrelevant.

PZ is reviewing your paper, and has explained the problems with it. Address those. Until and unless you actually recognize your mistakes, there is nothing else to discuss. Goodbye.

Checking the relative masses of different amino acids, I find that there are at least several hundred possible RNA codon tables that would be counted as artificial by ShCherbak and Makukov’s arbitrary criteria (due to things like isoleucine and leucine having the same molecular mass). That makes P(table|artificial) < 0.003, and most likely far less than that since the criteria as to what is considered artificial are flexible so the set of tables that would be considered artificial is probably actually measured in the hundreds of thousands.
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Given that and the chemical rules PZ described that constrain a naturally-evolved codon table to be one of a couple of hundred possibilities, the probability calculation actually goes like this:
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P(table is artificial) < 0.003*0.1/(0.003*0.1 + 0.004*0.9) = 0.08 and most likely P(table is artificial) much less than that. If P(table|artificial) is 1e-5, P(table is artificial) is 3e-4.
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Even if the prior probability P(artificial) were 0.5, P(table is artificial) would still be ~0.43 for P(table|artificial) = 0.003 and ~0.0025 for P(table|artificial) = 1e-5.
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And this is how the paper flagrantly misuses probability.

All prior evidence says that P(artificial) is much much less than P(natural).

I would like to stress again that we never say the table (the genetic code itself) is artificial. We are not ID proponents. We test the hypothesis of Crick and Orgel (also published in Icarus, by the way – do you feel comfortable with that?) and G.Marx (see my comment #89 here). We consider the genetic code merely as a biological media for a possible message. It does not contradict to the fact that the code has its direct biological functions and corresponding natural patterns. Or maybe you consider this hypothesis itself to be unscientific nonsense? If not, how do you take it into account in prior probabilities?
Anyway, returning to you formula, it would be just more correct in our case to say “this specific mapping of the code is artificial” rather than “the table itself is artificial”.

e.g. if P(table|artificial) = 0.01, so that there are 100 possible tables you would call artificial, and P(table|natural) = 0.004, since given the chemical rules PZ outlines above there are only a few hundred possible tables, and P(artificial) = 0.1, which is an overestimate based on previous claims of artificial signatures in biology,

P(table is artificial) = 0.01*0.1/(0.01*0.1 + 0.004*0.9) = 0.22.

I admit that you are probably better than me at Bayesian approach, but what I see here is just jiggling with numbers which I could call numerology ;)

And you do not have that evidence, since PZ has shown that P(table|natural) is quite high.

Let’s forget for a moment about our evidence and talk a little bit about traditional models of the code evolution and about what PZ actually wrote. PZ describes the degeneracy pattern and biosynthetic pattern in detail and gives it as an evidence against our conclusions. Strangely enough, he had missed that we mention not only the same patterns that he writes about, but actually much more. Here is the quote from our paper:

As soon as the genetic code was biochemically cracked (Nirenberg et al., 1965), its non-random structure became evident (Woese, 1965; Crick, 1968). The most obvious pattern that emerged in the code was its regular redundancy…. Apart from regular redundancy, a wealth of other features were reported afterwards, among which are robustness to errors (Alff-Steinberger, 1969), correlation between thermostability and redundancy of codon families (Lagerkvist, 1978), non-random distribution of amino acids among codons if judged by their polarity and bulkiness (Jungck, 1978), biosynthetic pathways (Taylor & Coates, 1989), reactivity (Siemion & Stefanowicz, 1992), and even taste (Zhuravlev, 2002). The code was also shown to be effective at handling additional information in DNA (Baisnée et al., 2001; Itzkovitz & Alon, 2007). Apparently, these features are related, if anything, to the direct biological function of the code.

And this is just a tiny fraction of patterns known to me, we did not have intention to list them all. So what? The problem is that when those patterns are found, they are readily recruited as a backup for one model of the code evolution or another, often even without any statistical testing. For example, what concerns correlation between the second letter and hydrophobicity of amino acid that PZ mentions – a simple computational test shows that almost each tenth randomly generated code will have a similar feature. And what concerns biosynthetic correlations, this model is the most controversial (compared to other traditional models) for the same reason of a lack in statistical evidence – see this paper, for example: http://www.pnas.org/content/97/25/13690.full.
If I knew nothing about the patterns described in our paper I would stick to the adaptive model of the code evolution, rather than to biosynthetic or stereochemical models (these are currently the three most popular models). Simply because the evidence for the adaptive model is most robust – the genetic code is very robust in terms of misreading (see this paper: http://link.springer.com/article/10.1007%2FPL00006381 ). But this feature does not contradict to our findings at all, and we write about that in the paper.

Checking the relative masses of different amino acids, I find that there are at least several hundred possible RNA codon tables that would be counted as artificial by ShCherbak and Makukov’s arbitrary criteria

1) And what is that “arbitrary criteria” that you refer to? I would appreciate if you could describe it a little bit in more detail.
2) Both you and PZ talk about nucleon patterns only. That is far not the only thing described in the paper. What about ideogram symmetries, semantical symmetries, the symbol of zero? Don’t you find that, together with all nucleon equalities which all turn out to have distinctive notation in a preferred numeral system is a little bit too much for such a small data set like the genetic code? Actually, in Appendix E we provide algebraic analysis and show that the mapping of the code itself is uniquely deduced from algebraic representation of all those patterns. I already mentioned it in the post #89, but you seem to be not impressed with that. But actually, if you show that an ensemble of patters employs informational capacity of the data set itself entirely, there is even actually no need in statistical testing: the “signal” is as strong as it possibly could.

I have no desire to engage you further on this matter, since you continue to miss the point. But so that it is abundantly clear to all readers, I will explain the probability calculation again.
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Above “table” refers to the real codon table, one particular way of mapping 64 possible three-base codons to 20 amino acids (21/22 in special cases) + Start + Stop.
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The “set of all possible tables” refers to all possible mappings of 64 codons to 22 different output states. This is a very large set. Within it, there are two interesting subsets. They are the “set of possible natural tables”, and the “set of possible artificial tables”.
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The “set of possible natural tables” is limited by what else we know about biochemistry. Given the rules that PZ and the biochemical literature outline, there are a couple hundred possible tables that were likely to have evolved naturally given the biochemistry that was around prior to the appearance of whatever could be called the first ribosomes. The real table is one of them. Different possible tables will be more or less likely, but absent additional information and for sake of illustration I assumed the probability distribution was uniform. This gives P(table|natural) = 1/(# possible natural tables) = 0.004 .
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This immediately shows that your statement that the null hypothesis was rejected with “P-value < 10^–13" is nonsense, or rather that you have formulated the null hypothesis incorrectly. The correct null hypothesis here is "the table developed by entirely natural evolutionary pathways". Given that the real table would be produced 0.4% of the time by natural evolution, you can never be more certain than that that it wasn't produced that way. To get actual probability that the table evolved naturally rather than artificially requires doing the Bayesian calculation, which gets to the other subset.
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The "set of possible artificial tables" is harder to quantify. The exact patterns in the real table are irrelevant here. We want the set of all tables that would include patterns that you would have considered as meeting any criteria for artificiality. That’s why I have a large range above: I don’t know the exact set of criteria the tables would need to meet. On the restrictive side, consider possible tables with exactly the same amino acid mass number for each codon. There’s a few hundred of those – shuffle around the 9 codons that map to leucine and isoleucine, with the constraint that you have at least one codon going to each amino acid. Taking off progressively more constraints, the number of possible artificial tables grows by orders of magnitude. So I gave the range above of a few hundred possible artificial tables to several hundred thousand, and again took a uniform distribution of the set. This gives the possibilities above, P(table|artificial) = 0.003 and P(table|artificial) = 1e-5. Even the latter is probably too high, because the criteria for what would be considered artificial are flexible (in theory, the set of possible artificial tables is equal to the set of all possible tables).
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Setting the prior probabilities P(artificial) and P(natural) is arguable. Maximum ignorance might say we should set them both equal to 0.5, a case I considered above. But we know that in every previous case where someone has claimed a feature of biology is artificial and not due to human interference, they have been proven wrong. This imposes a very high value for P(natural) and a correspondingly low value for P(artificial). Above, I assigned P(natural) = 0.9. This is a deliberate underestimate.
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Given all of that, I worked out the probability calculation. This is not numerology; it is basic statistical reasoning. Even in the best case for your proposal, the real table most likely evolved entirely naturally. Using more reasonable values that are still more favorable to you than is likely correct, P(artificial) = 0.1 and P(table|artificial) = 1e-5, gives P(table is artificial) is 3e-4. In other words, for those probability assignments, there is a 99.97% chance that you are wrong.

if you show that an ensemble of patterns employs informational capacity of the data set itself entirely, there is even actually no need in statistical testing: the “signal” is as strong as it possibly could.

“informational capacity” is irrelevant here. Of course the table contains information, and quite a lot of it – it reflects the underlying biochemistry. The question is where that information came from and, as has been explained, it almost certainly came entirely from entirely natural evolution.

If the codon table was entirely random, and not one of the set of possible natural tables, that would be more interesting.

The “set of possible natural tables” is limited by what else we know about biochemistry. Given the rules that PZ and the biochemical literature outline, there are a couple hundred possible tables that were likely to have evolved naturally

This is what I call an absolutely arbitrary and unfounded assumption. I couldn’t find similar statement in PZ’s post, and I don’t know where you took this information. If you get acquainted with the papers, especially review papers, on the genetic code published during last decade or so, you will find that there is no such limitation. Actually, the only plausible restriction for the set of possible natural (I would rather call them biologically viable, rather than natural) tables is the degeneracy pattern, which follows from thermodinamics of codon-anticodon interactions. That’s all. And that leaves us with ~ 10^30 possible biologically viable tables, out of ~10^83 all possible tables.

I’m not saying your statistical reasoning is incorrect. But the point is that you don’t have enough information (actual numbers to insert into the formula) to get the right answer simply because you are not familiar even with conventional models and ideas on the code evolution/organization.

And unfortunately you didn’t answer the most interesting point – your attitude to the hypothesis itself. If you accept that this hypothesis is scientific, do you think that your calculation effectively proves this hypothesis to be incorrect, regardless of what is actually found in the code?

Hey – that’t exactly the way our null hypothesis sounds. But since there are no deterministic evolutionary pathway (at least among models known to me), they are all stochastic in their nature, so they all involve chances anyway. The difference is in the trends assumed to be predominant (e.g., in adaptive model the evolution is driven primarily by natural selection for error minimization while in coevolution model it is driven by incorporation of amino acids into the code as new biosynthetic pathways appear). Therfore, we just define the null hypothesis with a little bit of clarification: “the table developed by entirely natural evolutionary pathways involving chances”.

That’s why I have a large range above: I don’t know the exact set of criteria the tables would need to meet.

Absolutely, and we mention this problem in Introduction. And for this reason we actually do not apply Bayesian approach. We just suggest to outline plausible prior restriction for the criterion (such as that considered parameters should not obviously be dependent on physical system of units, etc.) and just try to look. There is no another way here, if we accept Crick’s, Orgel’s and Marx’s hypothesis as working one.

I’m not saying your statistical reasoning is incorrect. But the point is that you don’t have enough information (actual numbers to insert into the formula) to get the right answer simply because you are not familiar even with conventional models and ideas on the code evolution/organization.

that argument sounds awfully familiar…

It sounds just like when theologists say that criticism of theology fails coming from people who haven’t read the “best” theology….

There’s a name for that, now what was it… ah yes! The Courtier’s Reply.

It sounds just like when theologists say that criticism of theology fails coming from people who haven’t read the “best” theology….

We are not talking here about theology, but about science. And there are no “best” papers on the genetic code, you are free to choose any one. But you will still not find an argument there which Michael used.

I suppose you never wondered why, after all this time, nobody did the same thing you just tried?

By the way, this is wrong. There were several attempts, for example here the one that was also published in Icarus: http://www.sciencedirect.com/science/article/pii/0019103579900940.
But the point is that those attempts considered DNA as a possible carrier, not the genetic code. And DNA is a worse candidate for that due to mutations.

Actually, I regularly read PZ Myers’ blog for a long time. And actually I would not interfere in the discussion if it were not for unethical behavior of some commentators who wished to lodge a complaint to Icarus editors. If you find the paper accepted for publications flawed – please, submit your own paper which shows the flaws of the original paper. This, I believe, would be a good scientific ethics.

If you find the paper accepted for publications flawed – please, submit your own paper which shows the flaws of the original paper. This, I believe, would be a good scientific ethics.

the flaws in your paper are laid entirely bare in the OP by PZ.

flaws which you are unable to respond to, because you think they are illegitimate if not published as a response in a peer reviewed journal.

While I agree that it isn’t for blogs to argue the value of scientific endeavor, this does NOT mean that a legitimate argument cannot be made in them.

you sir, need to address the criticisms directly yourself in this format if you wish to be heard here, instead of complaining about this being the wrong arena for it.

If you really believed what you said, you wouldn’t have bothered coming here to complain, so “shit or get off the pot” as they say. Either address the criticisms highlighted in the OP (NOT IN THE COMMENTS SECTION), or indeed shut up and wait for a response in the appropriate journal. One or the other.

Maxim, as I and others have stated at least once upthread, if you are going to argue the ID position you must (since you will be lead there by direct observation) also argue that this designer is either incompetent, evil, or some combination of both.

This is a case of missing the forest for the trees: even granted that the code is elegant (it is not, especially not in its workings) and designed, look at what the results are. What kind of sadistic designer would build a code like this?

Just for the record, they’ve responded to PZ’s critiquehere.
They claim that PZ don’t have “enough competence in the field of the genetic code”, what is odd since it’s not clear at all that both authors do have such competence.
It’s unclear also why they choose to publish in a journal not devoted to evolution or genetics (given that they are not pursuing such publications, if they are and the paper it’s still under review, this objections falls).

Gave the”encoded message idea” some thought and seem to agree with the basic idea that the organization given to define the number values used in the examples in a basic sense. That is, if something is “encoded” then some process of reorganization or assimilation might have to be employed to decrypt the info into some meaningful or recognizable pattern which if correct, and there truly is some form of embedded message, the result should be coherent to other known or defined information in some way which reveals to some extent its relevance or meaning.

With the above idea in mind I think it is somewhat stubborn and closed minded to suggest that an attempt to decipher or decode the “supposed” message is nothing more than numerology. In fact it is a rather proud and foolish way of thinking in my opinion since if there is in fact some hidden message embedded by aliens or a God or even some higher form of life then why would we want to miss any possible opportunity to discover such information.

It seems to me that people of faith or no faith have the same problem which I guess is a human condition and that is we are all to proud, stubborn or self righteous to invest our time in something which seems foolish to us personally based on our own limited understanding, which we seem to think has no limits, we are right no matter what just because that is how we think or believe.

It really is sad to think that people cannot see past their own intellectual weaknesses long enough to consider other possibilities. None of us have the answer to our origin at this point, at least in the context of what would be considered “mainstream” scientific empirical proof!! Although this says nothing of all the “evidence” that exists regarding that origin.

What really gets me too is that what difference does it make if there is a God behind our existence or not? Either way, what’s wrong with learning about evolution just because a person believes in God and what’s wrong with learning about God if you believe in evolution…? Just for the sake of being informed if nothing else. If there is a God maybe he used evolution to create us. Besides if there is a God with some purpose for us why would we want to miss that? If there is no God then we will still be informed in the ideas that caused man to think there is but still move forward scientifically.

There is nothing wrong with considering any idea if it is plausible and who are we to say what is actually possible or not? Btw, if you think you are the one to make such a call you are a total dumbass…

Since god doesn’t exist, there is no conclusive physical evidence for one, god is nothing but mental wanking. That’s why one can’t learn about imaginary deities (god). They are different in each mind, but have no basis in reality.

It really is sad to think that people cannot see past their own intellectual weaknesses long enough to consider other possibilities.

Speaking of intellectual weaknesses, you are an obvious idiot.

We did think about the truth claims of religions. That is why we are atheists!!! Most of us are ex-xians.

what’s wrong with learning about God

More from the idiot. Surveys show that atheists on average know more than xians about xianity. Learning more about religion is a proven pathway to atheism.

And which god anyway. There are thousands at least.

What really gets me too is that what difference does it make if there is a God behind our existence or not?

If it is the xian Sky Monster, the vast majority of humans will be tortured forever. If it is Brahma, we all get reincarnated based on our karma.

Disregarding the unprovable claims, it can matter a lot to everyone. Such as the hundreds of millions killed by one fanatic or another on an almost daily basis. Shiite versus Sunni in Iraq, the Boston marathon bombing, child witches executed in Africa, etc. Hardly a day goes by without a religious based atrocity somewhere. Hitchens rule. Religion poisons everything.

This is stupid. We consider all ideas and discard ones proven wrong. This is why we live in the space age instead of the stone age. In the present case, creationism/ID were falsified a few centuries ago. And they aren’t new, older than the invention of xianity.

and who are we to say what is actually possible or not? Btw, if you think you are the one to make such a call you are a total dumbass…

No!!! Cthulhu, you are dumb. We are scientists. We don’t guess or believe. We do experiments, collect data, and draw conclusions. And then we know.

For your imaginary deity to be plausible there must be solid and conclusive physical evidence for it. Now, if you have honesty and integrity like scientist do, YOU WILL EITHER PUT UP THE CONCLUSIVE EVIDENCE OR SHUT THE FUCK UP ABOUT YOUR IMAGINARY DEITY.

Nothing. In elementary school, we spent a great deal of time studying and comparing different pantheons, different gods, different creation myths (having some Hopi, Navajo, and Supai kids in my class helped (as did having a creative teacher (not to mention it was a small class and this was the 1970s))) including Abrahamic, many different Native American mythos, Buddism, Shinto, etc. I got to study, and present an oral report, on the Norse mythos (this was in fifth grade). Today, I enjoy reading about Christian heresies — both the early non-canonical gospels and the medieval heresies.

Comparative religion and history are a great way to learn about gods in all the different ways that humans have invented them. Insisting that the history of humanity’s gods somehow has a place in biology, genetics, evolution, geology, physics, mathematics, geophysics, or any other science is, how do I put this politely? absolute and total bullshit.

If anyone actually read my post you know I never said I believed in God, ( that’s your “assumption” and I’m not here to argue with you about why you don’t believe in God ). I do think “all manner” of scientific inquiry deserves equal attention where the “unknown” is the status quo… Also, as intellectual beings we should realize that we can’t possibly “know” or have any valid opinions regarding “the unknown” other than to say “it is unknown”. Therefore any comments that begin with an “assumption” are initially void and a waste of time to discuss no matter how argumentative and foolish their author may be. With this in mind how can we possibly “know” that some unorthodox method of examination, as with the DNA code, should be rejected, especially where the idea of encryption or encoding is concerned? We can’t… the possibilities are endless! If there “might” be another form of life which proceeded us and there “might” be some form of message embedded “somewhere” how can we know what the cipher is for said code? Again we can’t… This in itself justifies any “experimental” approach toward a possible solution. Because some choose not to consider “all” possibilities of our origin, God, alien or natural, doesn’t make those who do less scientific in their thinking, it makes them “open minded”. Just the opposite of stubborn people who “believe” they have answers to the “unknown”! Did you catch that word, “believe”… which is a “dogmatic religious view” rather than a scientific one…

Overy 3000 invented by humans 576man. There are a lot more than Yahweh.

Ya, but to my knowledge the Christian bible is the only book “proven” to contain actual prophecy which has and is coming true as we speak… If I’m going to choose a God I’d say the one in that prophetic book is the one I’ll go with.

“Disregarding the unprovable claims, it can matter a lot to everyone. Such as the hundreds of millions killed by one fanatic or another on an almost daily basis. Shiite versus Sunni in Iraq, the Boston marathon bombing, child witches executed in Africa, etc. Hardly a day goes by without a religious based atrocity somewhere. Hitchens rule. Religion poisons everything.”

This whole idea is as backward as it can be, just like most people who have little thought invested in “religious” ideas.

Whether there is a God or not of any kind it is still man’s fault for doing harm to each other… no one “controls” what we do as human beings, we “choose” our actions. If you actually apply the concept of man from a biblical perspective it makes sense whether we want to “believe” in that God or not.

“No!!! Cthulhu, you are dumb. We are scientists. We don’t guess or believe. We do experiments, collect data, and draw conclusions. And then we know.”

Not really… “scientists” don’t reject “possibilities” they entertain them and ponder experimental approaches to find the answers. People who know science but follow the money aren’t “scientists” they’re called puppets!

Because humans have “invented” the supposed appearances, traits or other requirements and the like of various gods doesn’t prove or even give evidence against whether there “actually” are spiritual entities as you “assume”. On the contrary, the various ideas conceived by people throughout history would, to some, give a strange indication that there may be something to such human ideas. If you think fairly and in an unbiased manner that is.

“Insisting that the history of humanity’s gods somehow has a place in biology, genetics, evolution, geology, physics, mathematics, geophysics, or any other science is, how do I put this politely? absolute and total bullshit.”

I don’t remember “insisting” anything like what you’re saying. All I am doing is suggesting that there are somethings still unknown and why should any of us reject various schools of thought, calling them “bullshit”, simply because we disagree with them. Why not entertain the ideas and see where they lead?

Just keep in mind we only know what we know, everything else is beyond our reasoning capabilities…

, you do realize that no proof that God exists isn’t proof that he doesn’t exist…? Right?

The Redhead is my wife. I’m bald. You are a fool. The null hypothesis is non-existence for things without evidence. Be they bigfoot, leprechans, or god. Those claiming god must show solid and conclusive physical evidence. Physical evidence that would pass muster with scientists, magicians, and professional debunkers as being of divine, and not natural (scientifically explained), origin. You present no evidence. Ergo, your claim of your imaginry deity existing is *floosh* sent to the sewer where it belongs, being unevidenced bullshit.

I do think “all manner” of scientific inquiry deserves equal attention where the “unknown” is the status quo

Science doesn’t give a shit what you “think”, or rather presuppose. If you can’t evidence your ideas, they are bullshit. Welcome to science, where your OPINION is *floosh* sewage.

If there “might” be another form of life which proceeded us

Hypotheticals are for loser philosophers. Not evidence based scientists. Might is irrelevant to what is.

Ya, but to my knowledge the Christian bible is the only book “proven” to contain actual prophecy which has and is coming true as we speak…

And yet you can’t supply one reference to back up your fuckwitted claim. Christopher Hittchens “that which is asserted without evidence can be dismissed without evidence.”. Anything based on a book of mythology fiction can be *floosh* sent to the sewer, until you prove conclusive evidence the babble is something other than mythology fiction. Your claims is irrelevant.

The point of that statement was very basic, why reject either?

Where the fuck is your solid and conclusive physical evidence for your imaginary deity? Compared to a million or so scientific papers backing evolution, directly and indirection? I’m still waiting for your first citation, as your OPINION will always be *floosh* dismissed as sewage without a link.

Like I said above, of things that are unknown everything is plausible.

Not made-up bullshit.

Are we supposed to consider Gandalf as a possible creator of some or all life, or is that just a little too much even for you?

Why not Santa Claus?

On the contrary, the various ideas conceived by people throughout history would, to some, give a strange indication that there may be something to such human ideas. If you think fairly and in an unbiased manner that is.

That is just meaningless tripe, you idiot.

You’re not considering Raven as a possibility are you? If not, you fail on your own “grounds.”

No you’re just very presumptuous. You don’t have to believe in something to support other peoples efforts or perspectives based on a scientific basis do you. Now why don’t you look at what I wrote for the purpose for which I wrote it and stop trying to twist it to mean what you want it to.

Ya, but to my knowledge the Christian bible is the only book “proven” to contain actual prophecy which has and is coming true as we speak… If I’m going to choose a God I’d say the one in that prophetic book is the one I’ll go with.

Wonder why these “prophecies” aren’t convincing to actual scholars. And no, I don’t need the idiotic notion that they just don’t want them to be true, as why wouldn’t they? It would be a much greater discovery if true than that they’re just vague tripe that people fit to the past as they desire. It’s just too obvious that it really is the latter.

Because humans have “invented” the supposed appearances, traits or other requirements and the like of various gods doesn’t prove or even give evidence against whether there “actually” are spiritual entities as you “assume”. On the contrary, the various ideas conceived by people throughout history would, to some, give a strange indication that there may be something to such human ideas. If you think fairly and in an unbiased manner that is.

If you think in a fair and unbiased manner, you realize that human imagination is unfair and very biased — biased towards thinking that what it imagines to be real is real.

So the first thing you should discount are entities that are imagined.

“Do we have any evidence that leprechauns and pink unicorns don’t exist?

Should we spend a lot of time and money investigating them?

How about the invisible dragon PZ Myers keeps in his garage?

Should we consider its existence as a serious possibility?

Should we consider the existence of PZ Myers’ invisible garage dragon as likely as the Christian God? More likely? Less likely? Why?”

Well if those creatures had the track record that the idea of God and religion has had throughout history I would say yes, but they don’t. The characteristic of being invisible isn’t a reason not to consider its existence. It may be that we have not discovered the proper way to reveal certain things. it is pure vanity and foolishness to “believe” that we in our limited knowledge can understand and know the unknown.

I would say that the dragon is infinitely less likely since it doesn’t have any credibility throughout history as long as there has been comunication like God and spirituality. Or a coherent book that was written by multiple writers over 4000 yrs or so but still has one theme from front to back which has to do with God and man. Oh ya and is prophetic in nature…

Also, there is the unknown, and then there is the unknown. That is to say, not all things are unknown to the same extent. Abiogenesis is an “unknown,” of course, but it isn’t woo, it’s something with extensive chemical and physical possibilities–and, importantly, limits. We can do science so long as we observe limits, so long as we take care to use demonstrable causes, not woo-crap.

If you found meaningful evidence for psychokinesis, then you’d have a genuine unknown, something that we really don’t understand at all, and we’d have to be more open to more possibilities, although not to just any made-up lies at all.

We explain the unknown with the known, however, rather than the obverse, which never works. That’s because of our possibilities for knowing, nothing to do with artificially limiting possibilities, it’s simply recognizing our limits. You want to “explain” using fiction, rather than following the only means that we have of explanation, finding distinct and observable causes for distinct and observable effects.

I guess so, it happened during Jesus’ life, over 300 prophecies were fulfilled in that alone. Start studying prophecy a little and watch the news just for entertainment sake if nothing else and see if you notice anything.

I would say that the dragon is infinitely less likely since it doesn’t have any credibility throughout history as long as there has been comunication like God and spirituality. Or a coherent book that was written by multiple writers over 4000 yrs or so but still has one theme from front to back which has to do with God and man. Oh ya and is prophetic in nature…

You REALLY need to learn about the persistence of the idea that dragons are real.

And I know I’m going to regret this but I’ll ask again. Exactly which biblical prophecies have come true and how were they fulfilled? Just one will do.

Ok, point taken, but if you know that don’t you think I know that too? So it should be obvious to “anyone” who isn’t a dumbass that I wasn’t referring to something so stupid. Why would people go off in left field when they are supposed to be discussing something in a “scientific” vein. Don’t be retarded. I’m really not trying to comment over stupid shit…

I’m beginning to think the people at this board are only here to argue they really don’t care about knowing or learning anything. What a waste of time…

Well if those creatures had the track record that the idea of God and religion has had throughout history I would say yes, but they don’t.

Ok, your god has a track record? What it is? There’s no proof of his existence.
I hope you are not seriously arguing that because lots of people believe in god the idea is plausible.
It’s not.
Although you do have a germ of truth there.
The *idea* of your particular god has a track record.
As a concept, it has lasted a few thousand years.
But the existence of the idea of god is not the same thing as your actual deity existing. I’m fairly certain the Greeks truly believed their gods existed as much as ancient Egyptians believed their deities existed.
Doesn’t mean they *did* exist.

The same amount of proof exists for your deity as there is for Zeus, Quetzalcoatl, Hermes, Thor, Heracles, Isis, Osiris.
You think your concept of god is plausible. Why? What makes that genocidal, sexist, baby killing asshole a more plausible deity than those worshipped by any of the *other* extant religions?

The characteristic of being invisible isn’t a reason not to consider its existence.

Uh, invisible…as well as intangible, inaudible, undetectable. According to xians, there is no way to detect yaweh’s existence (aside from the TOTES reliable “I know it in my heart” or “because reasons prayer). You have the burden of proof. You think your god exists, bring the evidence to the table. This is an extraordinary idea. It requires tremendous amounts of evidence. Evidence does not take the form of “lots of people believe” or “the idea has lasted a long time”. Lots of people once believed the world was flat (and it lasted a long time).

Oh, and as I’m sure you’ve been told, the existence of your god *has* been considered…and rejected because there is no evidence.

The burden of proof is the obligation of a party in an argument or dispute to provide sufficient evidence to shift the other party’s or a third party’s belief from their initial position. The burden of proof must be fulfilled by both establishing confirming evidence and negating oppositional evidence. Conclusions drawn from evidence may be subject to criticism based on a perceived failure to fulfill the burden of proof.

Two principle considerations are:

On whom does the burden of proof rest?
To what degree of certitude must the assertion be supported?

The latter question depends on the nature of the point under contention and determines the quantity and quality of evidence required to meet the burden of proof.

In a criminal trial in the United States, for example, the prosecution carries the burden of proof since the defendant is presumed innocent until proven guilty beyond a reasonable doubt. Similarly, in most civil procedures, the plaintiff carries the burden of proof and must convince a judge or jury that the preponderance of the evidence is on their side. Other legal standards of proof include “reasonable suspicion”, “probable cause” (as for arrest), “prima facie evidence”, “credible evidence”, “substantial evidence”, and “clear and convincing evidence”.

In a philosophical debate, there is an implicit burden of proof on the party asserting a claim, since the default position is generally one of neutrality or unbelief. Each party in a debate will therefore carry the burden of proof for any assertion they make in the argument, although some assertions may be granted by the other party without further evidence. If the debate is set up as a resolution to be supported by one side and refuted by another, the overall burden of proof is on the side supporting the resolution.http://en.wikipedia.org/wiki/Evidence#Burden_of_proof

emphasis mine.
Until you provide sufficient evidence for your particular god belief, the default position is unbelief. I do not believe in *ANY* deity (or anything “supernatural”). If the day arrives when ample evidence arises to prove that a specific deity exists, then I will amend my non belief. Until then, it makes no more sense to say that your god is real (or even plausible), than it is to say that you visit Never Never Land every weekend with Peter Pan.

“Wonder why these “prophecies” aren’t convincing to actual scholars. And no, I don’t need the idiotic notion that they just don’t want them to be true, as why wouldn’t they? It would be a much greater discovery if true than that they’re just vague tripe that people fit to the past as they desire. It’s just too obvious that it really is the latter.”

Well I don’t know about obvious, but you’re entitled to your thoughts. I really think it has more to do with doubting something so far fetched as miracles and raising from the dead stuff like that than not seeing the prophecies as being true. They doubt the miracles so discredit the writings.

It seems more “obvious” to me that there has to be something to it otherwise why would the world be so involved in it all throughout history? Think about it. Do you realize that the christian bible has been the best selling book for so long they don’t even included it in the comparison! It has sold 6 times more than any other book in history, approximately 6 billion copies… Dude that alone says something to me. Why would people buy a book that goes against everything we think or do if there wasn’t something goin on with it?

Anything without conclusive evidence, be it bigfoot or your imaginary deity, are in the null hypothesis as non-existent. Which means those claiming bigfoot or their deity exists, must provide the evidence, You provide nothing but blather, abject loser style. many words, no citations.

I guess so, it happened during Jesus’ life, over 300 prophecies were fulfilled in that alone.

Yet you can’t link to one showing what an abject losers you deists are. You lie and bullshit unless you show a link to evience to prove you are right. And your word is *floosh* sewage, and will remain sewage here.

“scientific” vein.

You are pretending to be “sciency” as a professional scientist, your unevidenced claims are all *floosh* dismissed as fuckwittery. There is no science of imaginary deities. There are only delusional fools who believe in non-existent things.

Do you realize that the christian bible has been the best selling book for so long they don’t even included it in the comparison! It has sold 6 times more than any other book in history, approximately 6 billion copies… Dude that alone says something to me.

Yes, and that’s why you’re incapable of engaging in any meaningful discussion.

Well I don’t know about obvious, but you’re entitled to your thoughts.

And we’re entitled to criticize the ravings of a delusional fool pretending to have something to say, but can’t evidence one claim. Those folks who can’t evidence claims are liars and bullshitters. Nothing you say is believed.

Science doesn’t give a shit about your or anybody else’s OPINIONS. Opinions are like assholes, every has one, and they often emit smelly things. Evidence is required in science. No evidence, no need to consider it, no matter what you delusionally think.

“Nonsense. Some unknowns would be consistent with reality as we see it; these are plausible for scientific and philosophical analysis and speculation.

Unknowns like an invisible person with magical superpowers would be inconsistent with reality as we see it, and so are very implausible.”

Not so, since they are unknown you can’t force the laws of our know reality upon those things unknown… you either attempt an explanation based on what is known or decide that you don’t have the knowledge to have an explanation, therefore concepts regarding the unknown remain plausible.

It seems to me that people of faith or no faith have the same problem which I guess is a human condition and that is we are all to proud, stubborn or self righteous to invest our time in something which seems foolish to us personally based on our own limited understanding, which we seem to think has no limits, we are right no matter what just because that is how we think or believe.

I’m sure we all have issues with what you said above.
However, it doesn’t relate to the existence of any deity. Looking at the evidence there is ZERO reason to believe any god or gods exists. I notice you focus solely on god, so I assume you must be referring to the genocidal butcher of the bible. Why do you ignore the possibility that any of a thousand other gods exist? Why is the focus of your “plausibility” limited to the xian god?
Also, you don’t know what people here believe, yet you’re trying to read minds. Accepting that the god hypothesis is not supported by evidence doesn’t make one close minded. Personally, I accept that my understanding is limited. I feel I am correct to not believe in gods, but that could change one day. It isn’t likely, because no god from any of the pantheons in human history has shown themselves, but hey, it’s *possible*. I won’t rule it out *completely*, because I know my understanding is limited. However, I go about my life as if none of the sky daddys or various pantheons exist because thus far, they’ve exerted no influence on the world.

What really gets me too is that what difference does it make if there is a God behind our existence or not? Either way, what’s wrong with learning about evolution just because a person believes in God and what’s wrong with learning about God if you believe in evolution…? Just for the sake of being informed if nothing else. If there is a God maybe he used evolution to create us. Besides if there is a God with some purpose for us why would we want to miss that? If there is no God then we will still be informed in the ideas that caused man to think there is but still move forward scientifically.

Why do you continue focusing on one particular god? You keep mentioning how “plausible” it is to believe in god, yet you never mention any *other* gods.
Also, plenty of people know about your god. They reject him. Even if he *did* exist, I would not want to worship him. He slaughtered nearly every living creature on the planet in a worldwide flood because he had a temper tantrum. He cursed all of humanity for the actions of two beings he created whom he *knew* were going to eat from the tree of knowledge. He calls for the rape of women. He’s fine with incest. He loves slavery. He’s fond of baby killing. He is a murderous scumbag. Yet, you want to entertain the possibility that he exists? That’s a deeply dumb idea.

Do you realize that the christian bible has been the best selling book for so long they don’t even included it in the comparison! It has sold 6 times more than any other book in history, approximately 6 billion copies… Dude that alone says something to me.

More idiocy from the godbotting idiot.

Fallacy of Argument from Popularity.

Just because a belief is popular doesn’t have any bearing on whether it is true. At one time the earth was Flat and orbited by the sun, both as false as creationism.

In point of fact, after 2,000 years, xians only make up 28% of the world’s population. And they are broken up into 42,000 sects that don’t agree on much of anything.

It also says the vast majority of those copies weren’t read. Including by you. The bible is a horrible book, a kludgy mess of obsolete morality such as stoning nonvirgin brides and disobedient children to death, slavery, and authoritarianism. Reading the bible is a good way to become an atheist.

these are plausible for scientific and philosophical analysis and speculation.

Science doesn’t speculate. If you have EVIDENCE, present it. If you don’t, shut the fuck up. That is what a person of honesty and integrity would do. And something godbots/creobots are incapable of. They lie and bullshit.

Not so, since they are unknown you can’t force the laws of our know reality upon those things unknown

And if they are unknown, they are ignored without evidence. What part of science needing evidence, not blather, are you having trouble with? Oh, the fact you have nothing of substance to evidence. As we know very well. That’s why science ignores imaginary deities. They add nothing but blather in incoherence.

Also, there is the unknown, and then there is the unknown. That is to say, not all things are unknown to the same extent. Abiogenesis is an “unknown,” of course, but it isn’t woo, it’s something with extensive chemical and physical possibilities–and, importantly, limits. We can do science so long as we observe limits, so long as we take care to use demonstrable causes, not woo-crap.

If you found meaningful evidence for psychokinesis, then you’d have a genuine unknown, something that we really don’t understand at all, and we’d have to be more open to more possibilities, although not to just any made-up lies at all.

We explain the unknown with the known, however, rather than the obverse, which never works. That’s because of our possibilities for knowing, nothing to do with artificially limiting possibilities, it’s simply recognizing our limits. You want to “explain” using fiction, rather than following the only means that we have of explanation, finding distinct and observable causes for distinct and observable effects.

Nice to have an intelligent answer.

Some things in science are based on probability and not fact so not all empirical evidence is truly empirical if you know what I mean. It appears thus so often that we have accepted the results as evidence for the outcome. The same could be said for the changes that take place in persons lives based on exposure to religion in the spiritual sense which bring forth known changes within the person, not all people but enough to accept as evidence to an open minded person. These non-physical evidences are just not accepted, I don’t know why not, they used to think they knew where electrons dwelt but now they know… they don’t know. We can’t even understand matter and we want to assume we know all there is to know. We really know nothing when it comes to certain things scientific or otherwise but I think we are too vain to accept it.

Sure it can, just shows your limited imagination… in the biblical sense God is “known” in the Spirit, in the sense he is “unknown” is in the physical…

There is no proof that they are “imagined” that is your opinion. Others are of the opinion that they are real. We do not have the ability to make those judgements for other people do we…?

We are already down to the Voices in People’s Heads fallacy.

Millions of people hear voices in their heads they claim come from god. Those voices all say completely different things.

All faith claims reduce down to voices in someone’s head.

Ya, but to my knowledge the Christian bible is the only book “proven” to contain actual prophecy which has and is coming true as we speak… If I’m going to choose a God I’d say the one in that prophetic book is the one I’ll go with.

This is false. A lie.

The xian bible is known to be mostly fiction. The prophecies that came true were written after the fact.

In point of fact, the bible is full of prophecies that never happened. One of the central tenets of jesus was the imminent Kingdom of god on earth. Jesus was supposed to come back almost immediately after being killed.

It never happened. It’s been 2,000 years, it’s predicted every year or so, and it will never happen.

Ad ignorantiam
The argument from ignorance basically states that a specific belief is true because we don’t know that it isn’t true. Defenders of extrasensory perception, for example, will often overemphasize how much we do not know about the human brain. It is therefore possible, they argue, that the brain may be capable of transmitting signals at a distance.

UFO proponents are probably the most frequent violators of this fallacy. Almost all UFO eyewitness evidence is ultimately an argument from ignorance – lights or objects sighted in the sky are unknown, and therefore they are alien spacecraft.

Intelligent design is almost entirely based upon this fallacy. The core argument for intelligent design is that there are biological structures that have not been fully explained by evolution, therefore a powerful intelligent designer must have created them.

Appeals to popularity suggest that an idea must be true simply because it is widely held. This is a fallacy because popular opinion can be, and quite often is, mistaken. Hindsight makes this clear: there were times when the majority of the population believed that the Earth is the still centre of the universe, and that diseases are caused by evil spirits; neither of these ideas was true, despite its popularity.
Example

(1) Most people believe in a god or ‘higher power’.
Therefore:
(2) God, or at least a higher power, must exist.

It doesn’t appear you know these fallacies, since you are employing them. Hell, you’ve giving some prime examples of logical fallacies.

There is no proof that they are “imagined” that is your opinion. Others are of the opinion that they are real. We do not have the ability to make those judgements for other people do we…?

You are seriously out of your depth here. Give up. People are free to believe what they want. If they want their opinions to be respected, they should make sure those beliefs are backed up with evidence.

There are people who believe that vaccinations cause autism. Such people have no proof to back up that *extremely* dangerous, and deadly belief.
There are people who believe that Bigfoot exists. They can’t provide any evidence of the creature, but swear it exists.
There are people who believe that they were abducted by aliens, yet for some reason, they cannot provide any proof.
There is no proof that the gods of Olympus ever existed. Without proof of them, there is no reason to believe they are real, nor should we even entertain the proposition that they are real. It would be unreasonable.

I personally think it is possible that there exists life beyond this planet. In fact, I think *that* is far more likely than any God Hypothesis humanity has crafted. At least we *know* that life has arisen in this universe (cause, look around), thus it is possible that other life could exist. However, I don’t have any proof. Until I do, the default position is that there is no other life.

I’m sure you don’t get the point yet, but simply having an opinion, especially one that is not backed up by reality, means exactly nothing. When you believe in (or entertain the possibility of) something that has no evidence, that idea should be mocked.

No I meant what I said. Even the part about not being here to argue with any dumdasses who could care less about science or learning anything on any subject.

My comments were to support all manner of research with regard to science not just ones people commonly used since certain things cannot be known you can’t know the proper method to use, that would be “experimental” then wouldn’t it.

Ok we disagree.. I say they don’t fail.Can’t force you to see it though.

Are you 12?
Damn, do you have any idea how idiotic you sound right now?
Of course you cannot convince anyone to see your way, because you don’t even know how to argue effectively. You have to bring facts, backed up by evidence to the table.
All you have is opinion…which is insufficient for winning an argument.
You lost long ago.

And I know I’m going to regret this but I’ll ask again. Exactly which biblical prophecies have come true and how were they fulfilled? Just one will do.

do some research

You’ve got nothing to say that is worthwhile.

The central theme of the NT was the coming Kingdom of god and/or heaven on earth.

It was supposed to be within a few years of when jesus was killed. It never happened. Today, the Apocalypse gets predicted all the time. There were 4 dates predicted in 2012 alone. They never happened, as usual.

Amuse us. Which of the 42,000 different sects are the One True Xian Cults? And how do you know which one? The stakes are high here. Pick the wrong one and you get sent to hell and tortured forever, or so they all claim.

I am broad minded. I accept as fact that which is broadly supported by real scientific evidence. Religious waffle and woo, not so much.

Ya I’m not religious either.

You believe one specific god out of thousands stands a chance of maybe, possibly existing. That is not supported by *any* “real scientific evidence”.
Perhaps you should try being close minded. Any more broad minded and you’re going to start believing you’re from Krypton.

You are pretending to be “sciency” as a professional scientist, your unevidenced claims are all *floosh* dismissed as fuckwittery. There is no science of imaginary deities. There are only delusional fools who believe in non-existent things.

No shortage of “opinions” here. leaves little to actually work with, as a “professional scientist” I mean. Science revolves around opinion as we all know…lol!

Haha! You said “in the biblical sense God is “known””, but “know” in the biblical sense means “fuck” !

(“And Adam knew Eve” — Gen. 4:1)

So you meant “fuck”!

(If you didn’t, you need to work on your writing skills)

My comments were to support all manner of research with regard to science not just ones people commonly used since certain things cannot be known you can’t know the proper method to use, that would be “experimental” then wouldn’t it.

Yes, I’m sure that you think that science should include the imaginary, the incoherent, the falsified and the make-believe.

And I know I’m going to regret this but I’ll ask again. Exactly which biblical prophecies have come true and how were they fulfilled? Just one will do.

do some research

That’s not how this works. If you make a positive claim it’s your job to back it up. Earlier you said Jesus fulfilled 300 prophecies, now you can’t be bothered to name one? Shouldn’t be a big task, just one specific prophecy that you can show has been fulfilled.

Ah, no surprise the chew toy couldn’t produce one piece of evidence to back any claim. Total word salad, with a side order of illogical arguments. When will they learn their unevidenced OPINION will always be *floosh* treated as the sewage it is.

576man
If you type
<blockquote>paste quoted text here</blockquote>
this will result.

paste quoted text here

It will make your comments easier to read.
It will not help you make sense.
—
I did some “research” and discovered that both the prophesies and the fulfillments are found in a “book” that has been rewritten, retranslated and reinterpreted hundreds of times in dozens of languages.
Ya think maybe that the accounts of both the prophesies and fulfillments might have been tweaked a bit?
If you print a bunch of books yourself and “sell” them to yourself, you don’t get to count it as a “best-seller”.

Looking at the evidence there is ZERO reason to believe any god or gods exists.

I totally disagree. The problem is what is acceptable as evidence to certain people. It is our own doubt and resistance to “unbelievable” things that hinders us. People who have experienced the “unbelievable” don’t have a problem with such concepts… That in itself is evidence. It is up to the 2nd party or hearer of such things to accept or reject the claims, where rejection makes them no less true.

Ok so you think I’m an idiot, I get it… That is because I disagree with you I suppose. People here are so sarcastic and dogmatic about their “own” beliefs it is ridicules…! It’s worse that any Christian or other religious person I have ever met.

How can a person ever hope to understand or learn anything with such an attitude?

Nope, it is because you keep making unevidenced claims, and when challenged, won’t put up, and won’t shut the fuck up, like people of honesty and integrity would do. Prima facie evidence that you lie and bullshit.

Science doesn’t speculate. If you have EVIDENCE, present it. If you don’t, shut the fuck up. That is what a person of honesty and integrity would do. And something godbots/creobots are incapable of. They lie and bullshit.

How can I have evidence for someone elses perspective such as the “supposed” DNA code when I don’t even understand fully their concept..? I chimed in just to support basic idea of scientific approaches to deciphering “possibly” encrypted data. Didn’t you read my original post?

The book of the religion of most of Europe of Europe’s colonies is very popular in Europe and Europe’s colonies, therefore… what?

What a stupid and short sited thing to say! 6 billion copies, that’s a copy for nearly “EVERYONE” on the freakin planet! 6 times the next most popular book “of all time” Mau sei tung or smoethin like that, of only 900,000,000. Must be popular in more places than Europe you think?

576man
If you type
<blockquote>paste quoted text here</blockquote>
this will result.

paste quoted text here

It will make your comments easier to read.
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Could someone else ask 576man about blockquotes.
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If you print a bunch of books yourself and “sell” them to yourself, you don’t get to count it as a “best-seller”.

What a stupid and short sited thing to say! 6 billion copies, that’s a copy for nearly “EVERYONE” on the freakin planet! 6 times the next most popular book “of all time” Mau sei tung or smoethin like that, of only 900,000,000. Must be popular in more places than Europe you think?

What an absurd version of the argument ad popular. Not all of those copies still exist. And there have been times and places when that book was one of the few that was allowed to be printed.

On the contrary, turn yours on and try to understand the idea you are not “all knowing”.

None of us are all-knowing. No one, nothing, is all-knowing. The way to learn new things is to follow evidence. Sometimes I’ll be wrong. Sometimes I won’t. Either way, I learn something new. So could you provide me with some evidence, any evidence, that shows the existence of any god or gods (doesn’t even have to be the evil Abrahamic version — any would do)? And if you could do it without using the Courtier’s Reply? That one is really old and has been done to death.

Could you provide me with some evidence, any evidence, that shows the existence of any god or gods (doesn’t even have to be the evil Abrahamic version — any would do)? And if you could do it without using the Courtier’s Reply this time?

and

Please blockquote. Even if all you learn is how to blockquote while you proselytize here to earn your godmerit points, this would be a plus for you.

No the real problem is that your beliefs or should I say disbeliefs hinder you from viewing certain things objectively.

I’m a scientist. I don’t have beliefs. I have evidenced conclusions. Beliefs are for those without evidence, like you. Beliefs are meaningless. They can and are often delusional. Which is why they are ignored.

26:15 Thus saith the Lord GOD to Tyrus; Shall not the isles shake at the sound of thy fall, when the wounded cry, when the slaughter is made in the midst of thee?
26:16 Then all the princes of the sea shall come down from their thrones, and lay away their robes, and put off their broidered garments: they shall clothe themselves with trembling; they shall sit upon the ground, and shall tremble at every moment, and be astonished at thee.
26:17 And they shall take up a lamentation for thee, and say to thee, How art thou destroyed, that wast inhabited of seafaring men, the renowned city, which wast strong in the sea, she and her inhabitants, which cause their terror to be on all that haunt it!
26:18 Now shall the isles tremble in the day of thy fall; yea, the isles that are in the sea shall be troubled at thy departure.
26:19 For thus saith the Lord GOD; When I shall make thee a desolate city, like the cities that are not inhabited; when I shall bring up the deep upon thee, and great waters shall cover thee;
26:20 When I shall bring thee down with them that descend into the pit, with the people of old time, and shall set thee in the low parts of the earth, in places desolate of old, with them that go down to the pit, that thou be not inhabited; and I shall set glory in the land of the living;
26:21 I will make thee a terror, and thou shalt be no more: though thou be sought for, yet shalt thou never be found again, saith the Lord GOD.

Well, Tyrus, though thou wast destroyed several times after this was written, thou hast been found, and it didn’t even take long.

Explain that.

they used to think they knew where electrons dwelt but now they know… they don’t know. We can’t even understand matter

You’ve misunderstood. It’s been clear since 1927 that electrons aren’t mathematical points, indeed that nothing has a position (or a velocity) that has infinite precision. Everything is smeared out. Not just our knowledge of things is imprecise, but the things themselves are smeared out.

Pictures like these don’t show you where the electron is 95 % of the time, as it’s sometimes wrongly explained. They show you where 95 % of the electron is, and where you going to find it with a probability of 95 % if you try to confine it.

People here are so sarcastic and dogmatic about their “own” beliefs[,] it is ridicul[ou]s…!

[…]

I chimed in just to support basic idea of scientific approaches to deciphering “possibly” encrypted data.

An honest question: do you know what quotation marks are used for? Some of your comments are difficult to read because your usage of them just makes no sense.

I didn’t come here try and prove God exists…

We know. You came here assuming that a very specific god exists, and we’re trying to get you to examine that assumption.

I do know of some interesting coincidences though.

Bring them on, once you’ve explained why Tyrus is the fourth largest city in Lebanon today.

Plato’s Republic also has a conversion experience recommended in it. One should become a born-again geometer.

Likely the historic source of the Xian conversion experience, in fact. Pythagoreanism, Plato, etc., the source in the West of some of the greatest concepts of mathematics and its applicability to nature, and also the source of the most useless concepts of relying upon mystical experiences for “truth.”

If there’s something you want to fault a lot of atheism for, it could be the fact that it tends not even to recognize “conversion” and mystical experiences and how they affect humans–except in a negative way. That’s said, though, and we move on to the fact is that “conversion” and personal mystical experiences, etc., have never been consistent across persons, cultures, and religions, often leading to contradictory notions, or to simply accepting contradiction as being somehow profound, not generally nonsense in the classical realm.

Yes, “conversion” and like experiences do affect people greatly in most cases. It’s reliable knowledge that has never demonstrably been gotten that way (creativity can occur in such states, true, but such creativity has to be subjected to sober analysis after one has “come down”), which is why we don’t rely upon it. Indeed, few believers in conversion and the mystical credit the experiences of those in other cultures and religions, except negatively, as Satanic or profoundly mistaken in some manner, for not agreeing with their own experiences.

Once we’ve taken account of the disagreement of mystical claims and the fact that nothing we can rely upon has come from it (at least without the usual “proving process” vetting the wild creative ideas), we simply can’t credit conversions and the like as providing reliable knowledge of anything, let alone something as unlikely as a god. Conversion, etc., is apparently simply evidence of mental states, even though those are often powerful experiences.

First, could you provide me with some evidence, any evidence, that shows the existence of any god or gods (doesn’t even have to be the evil Abrahamic version — any would do)? And if you could do it without using the Courtier’s Reply this time?

Second, could you please blockquote?

Third, Could you please try to understand that science deals with evidence, not proof. If you want proof, the mathematics department is on the top floor.

Fourth (okay, I’m an historian — numbers are not my long suit), could you define ‘spiritual’?

Maybe bout the time you learn there is no evidence that God “doesn’t” exist.

Oh! You use quotation marks for emphasis! That’s gonna get you misunderstood again and again and again, because they’re often used as scare quotes to indicate that something is not what the stuff between the scare quotes means.

So, you’re saying there’s no evidence that your very specific god doesn’t exist. But there’s also no evidence that there’s no invisible dragon in Carl Sagan’s garage. Should we believe everything there’s no evidence for?

I did some “research” and discovered that both the prophesies and the fulfillments are found in a “book” that has been rewritten, retranslated and reinterpreted hundreds of times in dozens of languages.
Ya think maybe that the accounts of both the prophesies and fulfillments might have been tweaked a bit?

See what I mean, no matter what someone says you people reject it as having been altered. It’s ridicules… Maybe such a thing could have happened but to go around with that presupposed notion regarding anything to do with God or religion is absurd… it’s circular to you people, “the evidence for God has been altered and can’t be trusted, therefore there is no evidence, therefore there is no God” How foolish…

I am not arguing that there is no god. I am stating that I have seen no evidence pointing to the possible existence of any god. You claim there is. You are making a positive claim. Back it up with evidence. Show that a god, any god, has directly affected earth. You make the claim, you need to back it up.

I didn’t even come here for this…

I think I know why you are here. You tried to convert us heathen scum but failed. Our hearts have been hardened. You tried. But you still get your “I proselytized to Atheists” button that you can show off at church.

And, just so you can continue to ignore me, have you even studies your cult?

What is ‘spiritual’? You keep using this word and I don’t know what you mean by it.

Also, please blockquote.

What evidence have you presented for the existence of any god or gods?

Nope, ill defined negatives, like you imaginary and ever changing definition of a deity, cannot be disproved. Only true non-thinkers would believe otherwise. Which is why the null hypothesis for your imaginary deity is non-existence. So you must supply POSITIVE EVIDENCE to change our minds. Physical evidence that would pass muster with scientists, magicians, and professional debunkers as being of divine, and not natural (scientifically explained), origin. Something equivalent to the eternally burning bush. Or, if you are honest and have integrity, knowing you don’t have that evidence, you shut the fuck up. Thanks for your prima facie evidence you are a liar and bullshitter, and you deity doesn’t exist except between your ears.

576man, How can we be expected to “prove” the nonexistence of your deity until you define precisely what your deity is? How would we distnguish it from an alien life form with an advanced technology? Or will you worship anything that can perform “magic” tricks?

Nope.
The people who printed them ‘bought’ them and gave them to other people who used them as toilet paper.
and seriously
You have never read a book on the history of the bible as a book?
Do you the the Christ family had a copy of the Old Testament?

See what I mean, no matter what someone says you people reject it as having been altered. It’s ridicules… Maybe such a thing could have happened but to go around with that presupposed notion regarding anything to do with God or religion is absurd

On the contrary, there is actual evidence that such a thing happened. It was quite common. Do you know who discovered that evidence? People who believed in God. People who believed in God read the Bible, analyzed its content, learned to read ancient Hebrew and read and compared ancient texts, looked at history and archaeology, and realized that any stunningly correct “prophecies” in the OT were made up after the fact.

Of course, the “prophecies” Christians claim are about Jesus, were about no such thing. In context they don’t even fit the Christian narrative all that well.

Why is Joseph claimed to be of the lineage of King David by two completely different genealogies, in Matthew vs. Luke?

Why is Jesus claimed to be of the lineage of King David at all when the whole point of Christian myth is that Joseph was not his father, which is told in the same damn chapters as those stupid genealogies?

The answer to those questions, as with many others about that sort of thing in the bible, is: “Because bullshit”.